semin-egor 0.9.0

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Files changed (38) hide show
  1. data/History.txt +49 -0
  2. data/Manifest.txt +37 -0
  3. data/PostInstall.txt +5 -0
  4. data/Rakefile +32 -0
  5. data/bin/egor +10 -0
  6. data/config/website.yml +2 -0
  7. data/config/website.yml.sample +2 -0
  8. data/egor.gemspec +51 -0
  9. data/lib/egor/cli.rb +1738 -0
  10. data/lib/egor/environment.rb +34 -0
  11. data/lib/egor/environment_class_hash.rb +20 -0
  12. data/lib/egor/environment_feature.rb +16 -0
  13. data/lib/egor/environment_feature_array.rb +12 -0
  14. data/lib/egor/heatmap_array.rb +111 -0
  15. data/lib/egor.rb +6 -0
  16. data/lib/math_extensions.rb +7 -0
  17. data/lib/narray_extensions.rb +22 -0
  18. data/lib/nmatrix_extensions.rb +245 -0
  19. data/lib/string_extensions.rb +17 -0
  20. data/script/console +10 -0
  21. data/script/destroy +14 -0
  22. data/script/generate +14 -0
  23. data/script/txt2html +71 -0
  24. data/test/test_egor.rb +11 -0
  25. data/test/test_egor_cli.rb +9 -0
  26. data/test/test_egor_environment_class_hash.rb +25 -0
  27. data/test/test_egor_environment_feature.rb +29 -0
  28. data/test/test_helper.rb +2 -0
  29. data/test/test_math_extensions.rb +11 -0
  30. data/test/test_narray_extensions.rb +14 -0
  31. data/test/test_nmatrix_extensions.rb +16 -0
  32. data/test/test_string_extensions.rb +11 -0
  33. data/website/index.html +16 -0
  34. data/website/index.txt +217 -0
  35. data/website/javascripts/rounded_corners_lite.inc.js +285 -0
  36. data/website/stylesheets/screen.css +158 -0
  37. data/website/template.html.erb +57 -0
  38. metadata +155 -0
data/test/test_egor_environment_feature.rb ADDED
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+ $:.unshift File.join(File.dirname(__FILE__), '..', 'lib', 'egor')
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+
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+ require 'test/unit'
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+ require 'environment_feature'
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+
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+ class TestEgorEnvironmentFeature < Test::Unit::TestCase
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+
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+ include Egor
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+
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+ def setup
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+ @env_ftr = EnvironmentFeature.new('Secondary Structure',
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+ 'HEPC'.split(''),
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+ 'HEPC'.split(''),
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+ 'T',
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+ 'F')
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+ end
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+
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+ def test_to_s
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+ assert_equal('Secondary Structure;HEPC;HEPC;T;F', @env_ftr.to_s)
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+ end
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+
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+ def test_constrained?
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+ assert(@env_ftr.constrained?)
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+ end
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+
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+ def silent?
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+ assert(!@env_ftr.silent?)
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+ end
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+ end
data/test/test_helper.rb ADDED
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+ require 'test/unit'
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+ require File.dirname(__FILE__) + '/../lib/egor'
data/test/test_math_extensions.rb ADDED
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+ $:.unshift File.join(File.dirname(__FILE__), "..", "lib")
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+
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+ require 'test/unit'
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+ require 'math_extensions'
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+
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+ class TestMathExtensions < Test::Unit::TestCase
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+
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+ def test_log2
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+ assert_equal(1, Math::log2(2))
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+ end
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+ end
data/test/test_narray_extensions.rb ADDED
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+ $:.unshift File.join(File.dirname(__FILE__), "..", "lib")
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+
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+ require "test/unit"
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+ require "narray_extensions"
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+
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+ class TestArrayExtensions < Test::Unit::TestCase
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+
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+ def test_pretty_string(opts={})
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+ m = NArray.float(3).indgen
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+ result ="# A B C\n" +
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+ "VAL 0.00 1.00 2.00"
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+ assert_equal(result, m.pretty_string(:col_header => %w[A B C], :row_header => 'VAL'))
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+ end
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+ end
data/test/test_nmatrix_extensions.rb ADDED
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+ $:.unshift File.join(File.dirname(__FILE__), "..", "lib")
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+
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+ require "test/unit"
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+ require "nmatrix_extensions"
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+
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+ class TestNmatrixExtensions < Test::Unit::TestCase
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+
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+ def test_pretty_string(opts={})
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+ m = NMatrix.float(3,3).indgen
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+ result ="# A B C\n" +
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+ "VAL 0.00 1.00 2.00\n" +
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+ " 3.00 4.00 5.00\n" +
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+ " 6.00 7.00 8.00"
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+ assert_equal(result, m.pretty_string(:col_header => %w[A B C], :row_header => %w[VAL]))
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+ end
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+ end
data/test/test_string_extensions.rb ADDED
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+ $:.unshift File.join(File.dirname(__FILE__), "..", "lib")
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+
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+ require "test/unit"
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+ require "string_extensions"
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+
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+ class TestStringExtensions < Test::Unit::TestCase
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+
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+ def test_remove_internal_spaces
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+ assert_equal("hellosemin", "he ll o\r\n sem in\r \n".remove_internal_spaces)
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+ end
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+ end
data/website/index.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Refresh" content="5; URL=http://github.com/semin/egor">
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+ <title>
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+ egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
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+ </title>
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+ </head>
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+ <body>
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+ <p>
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+ An official web site for Egor will be available when our new web server is ready. Until then, this page will be redirected to its Git repository, <a href="http://rubyforge.org/projects/egor/">http://github.com/semin/egor</a> in 5 seconds.
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+ </p>
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+ - Semin
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+ </body>
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+ </html>
data/website/index.txt ADDED
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+ h1. egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
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+
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+ h2. Description
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+
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+ 'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.
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+
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+
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+ h2. Features
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+
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+ * Environment-specific substitution table generation based on user providing environmental class definition
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+ * Entropy-based smoothing procedures to cope with sparse data problem
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+ * BLOSUM-like weighting procedures using PID threshold
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+ * Both unidirectional and bidirectional substitution matirces can be generated
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+
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+
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+ h2. Installation
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+
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+ <pre>
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+ ~user $ sudo gem install egor
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+ </pre>
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+
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+
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+ h2. Requirements
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+
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+ * ruby 1.8.7 or above (http://www.ruby-lang.org)
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+ * rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
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+
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+ Following RubyGems will be automatically installed if you have rubygems installed on your machine
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+
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+ * narray (http://narray.rubyforge.org/)
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+ * facets (http://facets.rubyforge.org/)
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+ * bio (http://bioruby.open-bio.org/)
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+ * simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
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+
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+
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+ h2. Basic Usage
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+
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+ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/), so in most cases, you can swap 'subst' with 'egor'.
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST-file -c classdef.dat
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+ or
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+ ~user $ egor -l TEM-file -c classdef.dat
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+ </pre>
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+
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+
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+ h2. Options
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+
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+ <pre>
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+ --tem-file (-f) FILE: a tem file
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+ --tem-list (-l) FILE: a list for tem files
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+ --classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
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+ --outfile (-o) FILE: output filename (default 'allmat.dat')
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+ --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
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+ --noweight: calculate substitution count with no weights
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+ --smooth (-s) INTEGER:
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+ 0 for partial smoothing (default)
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+ 1 for full smoothing
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+ --p1smooth: perform smoothing for p1 probability calculation when partial smoothing
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+ --nosmooth: perform no smoothing operation
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+ --cys (-y) INTEGER:
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+ 0 for using C and J only for structure (default)
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+ 1 for both structure and sequence
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+ 2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
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+ --output INTEGER:
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+ 0 for raw count (no smoothing performed)
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+ 1 for probabilities
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+ 2 for log odds ratios (default)
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+ --noroundoff: do not round off log odds ratio
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+ --scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
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+ --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
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+ --autosigma: automatically adjust the sigma value for smoothing
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+ --add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
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+ --penv: use environment-dependent frequencies for log odds ratio calculation (default false) (NOT implemented yet!!!)
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+ --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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+ --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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+ --verbose (-v) INTEGER
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+ 0 for ERROR level
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+ 1 for WARN or above level (default)
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+ 2 for INFO or above level
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+ 3 for DEBUG or above level
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+ --version: print version
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+ --help (-h): show help
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+ </pre>
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+
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+
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+ h2. Usage
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+
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+ h4. 1. Prepare an environmental class definition file.
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+
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+ <pre>
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+ ~user $ cat classdef.dat
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+ #
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+ # name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);\
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+ # constrained or not (T or F); silent (used as masks)? (T or F)
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+ #
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+ secondary structure and phi angle;HEPC;HEPC;T;F
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+ solvent accessibility;TF;Aa;F;F
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+ hydrogen bond to other sidechain/heterogen;TF;Ss;F;F
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+ hydrogen bond to mainchain CO;TF;Oo;F;F
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+ hydrogen bond to mainchain NH;TF;Nn;F;F
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+ </pre>
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+
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+ h4. 2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
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+
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+ <pre>
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+ ~user $ cat sample1.tem
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+ >P1;1mnma
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+ sequence
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+ QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
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+ IQACLNAPDD*
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+ >P1;1egwa
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+ sequence
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+ --GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
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+ ----------*
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+ >P1;1mnma
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+ secondary structure and phi angle
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+ CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
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+ HHHHHCCCCP*
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+ >P1;1egwa
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+ secondary structure and phi angle
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+ --CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
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+ ----------*
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+ >P1;1mnma
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+ solvent accessibility
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+ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
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+ TTTTTTTTTT*
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+ >P1;1egwa
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+ solvent accessibility
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+ --TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
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+ ----------*
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+ ...
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+ </pre>
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+
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+ h4. 3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
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+
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+ <pre>
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+ ~user $ ls -1 *.tem > TEMLIST
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+ ~user $ cat TEMLIST
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+ sample1.tem
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+ sample2.tem
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+ ...
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+ </pre>
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+
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+ h4. 4. To produce substitution count matrices, type
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST --output 0 -o substcount.mat
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+ </pre>
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+
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+ h4. 5. To produce substitution probability matrices, type
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST --output 1 -o substprob.mat
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+ </pre>
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+
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+ h4. 6. To produce log odds ratio matrices, type
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST --output 2 -o substlogo.mat
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+ </pre>
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+
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+ h4. 7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST --pidmin 60 --pidmax 80 --output 1
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+ </pre>
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+
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+ h4. 8. To change the clustering level (default 60), type
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+
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+ <pre>
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+ ~user $ egor -l TEMLIST --weight 80 --output 2
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+ </pre>
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+
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+ h4. 9. In case any positions are masked with the character 'X' in any environmental feature will be excluded from the calculation of substitution counts.
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+
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+
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+ h2. Repository
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+
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+ You can download a pre-built RubyGems package from
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+
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+ * rubyforge: "http://rubyforge.org/projects/egor":http://rubyforge.org/projects/egor
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+
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+ or, You can fetch the source from
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+
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+ * github: "http://github.com/semin/egor/tree/master":http://github.com/semin/egor/tree/master
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+
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+
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+ h2. Contact
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+
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+ Comments are welcome, please send an email to me (seminlee at gmail dot com).
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+
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+
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+ h2. License
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+
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+ (The MIT License)
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+
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+ Copyright (c) 2008 Semin Lee
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ 'Software'), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/website/javascripts/rounded_corners_lite.inc.js ADDED
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+
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+ /****************************************************************
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+ * *
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+ * curvyCorners *
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+ * ------------ *
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+ * *
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+ * This script generates rounded corners for your divs. *
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+ * *
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+ * Version 1.2.9 *
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+ * Copyright (c) 2006 Cameron Cooke *
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+ * By: Cameron Cooke and Tim Hutchison. *
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+ * *
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+ * *
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+ * Website: http://www.curvycorners.net *
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+ * Email: info@totalinfinity.com *
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+ * Forum: http://www.curvycorners.net/forum/ *
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+ * *
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+ * *
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+ * This library is free software; you can redistribute *
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+ * it and/or modify it under the terms of the GNU *
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+ * Lesser General Public License as published by the *
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+ * Free Software Foundation; either version 2.1 of the *
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+ * License, or (at your option) any later version. *
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+ * *
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+ * This library is distributed in the hope that it will *
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+ * be useful, but WITHOUT ANY WARRANTY; without even the *
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+ * implied warranty of MERCHANTABILITY or FITNESS FOR A *
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+ * PARTICULAR PURPOSE. See the GNU Lesser General Public *
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+ * License for more details. *
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+ * *
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+ * You should have received a copy of the GNU Lesser *
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+ * General Public License along with this library; *
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+ * Inc., 59 Temple Place, Suite 330, Boston, *
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+ * MA 02111-1307 USA *
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+ * *
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+ ****************************************************************/
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+
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+ var isIE = navigator.userAgent.toLowerCase().indexOf("msie") > -1; var isMoz = document.implementation && document.implementation.createDocument; var isSafari = ((navigator.userAgent.toLowerCase().indexOf('safari')!=-1)&&(navigator.userAgent.toLowerCase().indexOf('mac')!=-1))?true:false; function curvyCorners()
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+ { if(typeof(arguments[0]) != "object") throw newCurvyError("First parameter of curvyCorners() must be an object."); if(typeof(arguments[1]) != "object" && typeof(arguments[1]) != "string") throw newCurvyError("Second parameter of curvyCorners() must be an object or a class name."); if(typeof(arguments[1]) == "string")
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+ { var startIndex = 0; var boxCol = getElementsByClass(arguments[1]);}
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+ else
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+ { var startIndex = 1; var boxCol = arguments;}
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+ var curvyCornersCol = new Array(); if(arguments[0].validTags)
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+ var validElements = arguments[0].validTags; else
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+ var validElements = ["div"]; for(var i = startIndex, j = boxCol.length; i < j; i++)
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+ { var currentTag = boxCol[i].tagName.toLowerCase(); if(inArray(validElements, currentTag) !== false)
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+ { curvyCornersCol[curvyCornersCol.length] = new curvyObject(arguments[0], boxCol[i]);}
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+ }
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+ this.objects = curvyCornersCol; this.applyCornersToAll = function()
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+ { for(var x = 0, k = this.objects.length; x < k; x++)
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+ { this.objects[x].applyCorners();}
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+ }
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+ }
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+ function curvyObject()
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+ { this.box = arguments[1]; this.settings = arguments[0]; this.topContainer = null; this.bottomContainer = null; this.masterCorners = new Array(); this.contentDIV = null; var boxHeight = get_style(this.box, "height", "height"); var boxWidth = get_style(this.box, "width", "width"); var borderWidth = get_style(this.box, "borderTopWidth", "border-top-width"); var borderColour = get_style(this.box, "borderTopColor", "border-top-color"); var boxColour = get_style(this.box, "backgroundColor", "background-color"); var backgroundImage = get_style(this.box, "backgroundImage", "background-image"); var boxPosition = get_style(this.box, "position", "position"); var boxPadding = get_style(this.box, "paddingTop", "padding-top"); this.boxHeight = parseInt(((boxHeight != "" && boxHeight != "auto" && boxHeight.indexOf("%") == -1)? boxHeight.substring(0, boxHeight.indexOf("px")) : this.box.scrollHeight)); this.boxWidth = parseInt(((boxWidth != "" && boxWidth != "auto" && boxWidth.indexOf("%") == -1)? boxWidth.substring(0, boxWidth.indexOf("px")) : this.box.scrollWidth)); this.borderWidth = parseInt(((borderWidth != "" && borderWidth.indexOf("px") !== -1)? borderWidth.slice(0, borderWidth.indexOf("px")) : 0)); this.boxColour = format_colour(boxColour); this.boxPadding = parseInt(((boxPadding != "" && boxPadding.indexOf("px") !== -1)? boxPadding.slice(0, boxPadding.indexOf("px")) : 0)); this.borderColour = format_colour(borderColour); this.borderString = this.borderWidth + "px" + " solid " + this.borderColour; this.backgroundImage = ((backgroundImage != "none")? backgroundImage : ""); this.boxContent = this.box.innerHTML; if(boxPosition != "absolute") this.box.style.position = "relative"; this.box.style.padding = "0px"; if(isIE && boxWidth == "auto" && boxHeight == "auto") this.box.style.width = "100%"; if(this.settings.autoPad == true && this.boxPadding > 0)
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+ this.box.innerHTML = ""; this.applyCorners = function()
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+ { for(var t = 0; t < 2; t++)
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+ { switch(t)
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+ { case 0:
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+ if(this.settings.tl || this.settings.tr)
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+ { var newMainContainer = document.createElement("DIV"); newMainContainer.style.width = "100%"; newMainContainer.style.fontSize = "1px"; newMainContainer.style.overflow = "hidden"; newMainContainer.style.position = "absolute"; newMainContainer.style.paddingLeft = this.borderWidth + "px"; newMainContainer.style.paddingRight = this.borderWidth + "px"; var topMaxRadius = Math.max(this.settings.tl ? this.settings.tl.radius : 0, this.settings.tr ? this.settings.tr.radius : 0); newMainContainer.style.height = topMaxRadius + "px"; newMainContainer.style.top = 0 - topMaxRadius + "px"; newMainContainer.style.left = 0 - this.borderWidth + "px"; this.topContainer = this.box.appendChild(newMainContainer);}
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+ break; case 1:
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+ if(this.settings.bl || this.settings.br)
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+ { var newMainContainer = document.createElement("DIV"); newMainContainer.style.width = "100%"; newMainContainer.style.fontSize = "1px"; newMainContainer.style.overflow = "hidden"; newMainContainer.style.position = "absolute"; newMainContainer.style.paddingLeft = this.borderWidth + "px"; newMainContainer.style.paddingRight = this.borderWidth + "px"; var botMaxRadius = Math.max(this.settings.bl ? this.settings.bl.radius : 0, this.settings.br ? this.settings.br.radius : 0); newMainContainer.style.height = botMaxRadius + "px"; newMainContainer.style.bottom = 0 - botMaxRadius + "px"; newMainContainer.style.left = 0 - this.borderWidth + "px"; this.bottomContainer = this.box.appendChild(newMainContainer);}
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+ break;}
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+ }
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+ if(this.topContainer) this.box.style.borderTopWidth = "0px"; if(this.bottomContainer) this.box.style.borderBottomWidth = "0px"; var corners = ["tr", "tl", "br", "bl"]; for(var i in corners)
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+ { if(i > -1 < 4)
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+ { var cc = corners[i]; if(!this.settings[cc])
70
+ { if(((cc == "tr" || cc == "tl") && this.topContainer != null) || ((cc == "br" || cc == "bl") && this.bottomContainer != null))
71
+ { var newCorner = document.createElement("DIV"); newCorner.style.position = "relative"; newCorner.style.fontSize = "1px"; newCorner.style.overflow = "hidden"; if(this.backgroundImage == "")
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+ newCorner.style.backgroundColor = this.boxColour; else
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+ newCorner.style.backgroundImage = this.backgroundImage; switch(cc)
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+ { case "tl":
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+ newCorner.style.height = topMaxRadius - this.borderWidth + "px"; newCorner.style.marginRight = this.settings.tr.radius - (this.borderWidth*2) + "px"; newCorner.style.borderLeft = this.borderString; newCorner.style.borderTop = this.borderString; newCorner.style.left = -this.borderWidth + "px"; break; case "tr":
76
+ newCorner.style.height = topMaxRadius - this.borderWidth + "px"; newCorner.style.marginLeft = this.settings.tl.radius - (this.borderWidth*2) + "px"; newCorner.style.borderRight = this.borderString; newCorner.style.borderTop = this.borderString; newCorner.style.backgroundPosition = "-" + (topMaxRadius + this.borderWidth) + "px 0px"; newCorner.style.left = this.borderWidth + "px"; break; case "bl":
77
+ newCorner.style.height = botMaxRadius - this.borderWidth + "px"; newCorner.style.marginRight = this.settings.br.radius - (this.borderWidth*2) + "px"; newCorner.style.borderLeft = this.borderString; newCorner.style.borderBottom = this.borderString; newCorner.style.left = -this.borderWidth + "px"; newCorner.style.backgroundPosition = "-" + (this.borderWidth) + "px -" + (this.boxHeight + (botMaxRadius + this.borderWidth)) + "px"; break; case "br":
78
+ newCorner.style.height = botMaxRadius - this.borderWidth + "px"; newCorner.style.marginLeft = this.settings.bl.radius - (this.borderWidth*2) + "px"; newCorner.style.borderRight = this.borderString; newCorner.style.borderBottom = this.borderString; newCorner.style.left = this.borderWidth + "px"
79
+ newCorner.style.backgroundPosition = "-" + (botMaxRadius + this.borderWidth) + "px -" + (this.boxHeight + (botMaxRadius + this.borderWidth)) + "px"; break;}
80
+ }
81
+ }
82
+ else
83
+ { if(this.masterCorners[this.settings[cc].radius])
84
+ { var newCorner = this.masterCorners[this.settings[cc].radius].cloneNode(true);}
85
+ else
86
+ { var newCorner = document.createElement("DIV"); newCorner.style.height = this.settings[cc].radius + "px"; newCorner.style.width = this.settings[cc].radius + "px"; newCorner.style.position = "absolute"; newCorner.style.fontSize = "1px"; newCorner.style.overflow = "hidden"; var borderRadius = parseInt(this.settings[cc].radius - this.borderWidth); for(var intx = 0, j = this.settings[cc].radius; intx < j; intx++)
87
+ { if((intx +1) >= borderRadius)
88
+ var y1 = -1; else
89
+ var y1 = (Math.floor(Math.sqrt(Math.pow(borderRadius, 2) - Math.pow((intx+1), 2))) - 1); if(borderRadius != j)
90
+ { if((intx) >= borderRadius)
91
+ var y2 = -1; else
92
+ var y2 = Math.ceil(Math.sqrt(Math.pow(borderRadius,2) - Math.pow(intx, 2))); if((intx+1) >= j)
93
+ var y3 = -1; else
94
+ var y3 = (Math.floor(Math.sqrt(Math.pow(j ,2) - Math.pow((intx+1), 2))) - 1);}
95
+ if((intx) >= j)
96
+ var y4 = -1; else
97
+ var y4 = Math.ceil(Math.sqrt(Math.pow(j ,2) - Math.pow(intx, 2))); if(y1 > -1) this.drawPixel(intx, 0, this.boxColour, 100, (y1+1), newCorner, -1, this.settings[cc].radius); if(borderRadius != j)
98
+ { for(var inty = (y1 + 1); inty < y2; inty++)
99
+ { if(this.settings.antiAlias)
100
+ { if(this.backgroundImage != "")
101
+ { var borderFract = (pixelFraction(intx, inty, borderRadius) * 100); if(borderFract < 30)
102
+ { this.drawPixel(intx, inty, this.borderColour, 100, 1, newCorner, 0, this.settings[cc].radius);}
103
+ else
104
+ { this.drawPixel(intx, inty, this.borderColour, 100, 1, newCorner, -1, this.settings[cc].radius);}
105
+ }
106
+ else
107
+ { var pixelcolour = BlendColour(this.boxColour, this.borderColour, pixelFraction(intx, inty, borderRadius)); this.drawPixel(intx, inty, pixelcolour, 100, 1, newCorner, 0, this.settings[cc].radius, cc);}
108
+ }
109
+ }
110
+ if(this.settings.antiAlias)
111
+ { if(y3 >= y2)
112
+ { if (y2 == -1) y2 = 0; this.drawPixel(intx, y2, this.borderColour, 100, (y3 - y2 + 1), newCorner, 0, 0);}
113
+ }
114
+ else
115
+ { if(y3 >= y1)
116
+ { this.drawPixel(intx, (y1 + 1), this.borderColour, 100, (y3 - y1), newCorner, 0, 0);}
117
+ }
118
+ var outsideColour = this.borderColour;}
119
+ else
120
+ { var outsideColour = this.boxColour; var y3 = y1;}
121
+ if(this.settings.antiAlias)
122
+ { for(var inty = (y3 + 1); inty < y4; inty++)
123
+ { this.drawPixel(intx, inty, outsideColour, (pixelFraction(intx, inty , j) * 100), 1, newCorner, ((this.borderWidth > 0)? 0 : -1), this.settings[cc].radius);}
124
+ }
125
+ }
126
+ this.masterCorners[this.settings[cc].radius] = newCorner.cloneNode(true);}
127
+ if(cc != "br")
128
+ { for(var t = 0, k = newCorner.childNodes.length; t < k; t++)
129
+ { var pixelBar = newCorner.childNodes[t]; var pixelBarTop = parseInt(pixelBar.style.top.substring(0, pixelBar.style.top.indexOf("px"))); var pixelBarLeft = parseInt(pixelBar.style.left.substring(0, pixelBar.style.left.indexOf("px"))); var pixelBarHeight = parseInt(pixelBar.style.height.substring(0, pixelBar.style.height.indexOf("px"))); if(cc == "tl" || cc == "bl"){ pixelBar.style.left = this.settings[cc].radius -pixelBarLeft -1 + "px";}
130
+ if(cc == "tr" || cc == "tl"){ pixelBar.style.top = this.settings[cc].radius -pixelBarHeight -pixelBarTop + "px";}
131
+ switch(cc)
132
+ { case "tr":
133
+ pixelBar.style.backgroundPosition = "-" + Math.abs((this.boxWidth - this.settings[cc].radius + this.borderWidth) + pixelBarLeft) + "px -" + Math.abs(this.settings[cc].radius -pixelBarHeight -pixelBarTop - this.borderWidth) + "px"; break; case "tl":
134
+ pixelBar.style.backgroundPosition = "-" + Math.abs((this.settings[cc].radius -pixelBarLeft -1) - this.borderWidth) + "px -" + Math.abs(this.settings[cc].radius -pixelBarHeight -pixelBarTop - this.borderWidth) + "px"; break; case "bl":
135
+ pixelBar.style.backgroundPosition = "-" + Math.abs((this.settings[cc].radius -pixelBarLeft -1) - this.borderWidth) + "px -" + Math.abs((this.boxHeight + this.settings[cc].radius + pixelBarTop) -this.borderWidth) + "px"; break;}
136
+ }
137
+ }
138
+ }
139
+ if(newCorner)
140
+ { switch(cc)
141
+ { case "tl":
142
+ if(newCorner.style.position == "absolute") newCorner.style.top = "0px"; if(newCorner.style.position == "absolute") newCorner.style.left = "0px"; if(this.topContainer) this.topContainer.appendChild(newCorner); break; case "tr":
143
+ if(newCorner.style.position == "absolute") newCorner.style.top = "0px"; if(newCorner.style.position == "absolute") newCorner.style.right = "0px"; if(this.topContainer) this.topContainer.appendChild(newCorner); break; case "bl":
144
+ if(newCorner.style.position == "absolute") newCorner.style.bottom = "0px"; if(newCorner.style.position == "absolute") newCorner.style.left = "0px"; if(this.bottomContainer) this.bottomContainer.appendChild(newCorner); break; case "br":
145
+ if(newCorner.style.position == "absolute") newCorner.style.bottom = "0px"; if(newCorner.style.position == "absolute") newCorner.style.right = "0px"; if(this.bottomContainer) this.bottomContainer.appendChild(newCorner); break;}
146
+ }
147
+ }
148
+ }
149
+ var radiusDiff = new Array(); radiusDiff["t"] = Math.abs(this.settings.tl.radius - this.settings.tr.radius)
150
+ radiusDiff["b"] = Math.abs(this.settings.bl.radius - this.settings.br.radius); for(z in radiusDiff)
151
+ { if(z == "t" || z == "b")
152
+ { if(radiusDiff[z])
153
+ { var smallerCornerType = ((this.settings[z + "l"].radius < this.settings[z + "r"].radius)? z +"l" : z +"r"); var newFiller = document.createElement("DIV"); newFiller.style.height = radiusDiff[z] + "px"; newFiller.style.width = this.settings[smallerCornerType].radius+ "px"
154
+ newFiller.style.position = "absolute"; newFiller.style.fontSize = "1px"; newFiller.style.overflow = "hidden"; newFiller.style.backgroundColor = this.boxColour; switch(smallerCornerType)
155
+ { case "tl":
156
+ newFiller.style.bottom = "0px"; newFiller.style.left = "0px"; newFiller.style.borderLeft = this.borderString; this.topContainer.appendChild(newFiller); break; case "tr":
157
+ newFiller.style.bottom = "0px"; newFiller.style.right = "0px"; newFiller.style.borderRight = this.borderString; this.topContainer.appendChild(newFiller); break; case "bl":
158
+ newFiller.style.top = "0px"; newFiller.style.left = "0px"; newFiller.style.borderLeft = this.borderString; this.bottomContainer.appendChild(newFiller); break; case "br":
159
+ newFiller.style.top = "0px"; newFiller.style.right = "0px"; newFiller.style.borderRight = this.borderString; this.bottomContainer.appendChild(newFiller); break;}
160
+ }
161
+ var newFillerBar = document.createElement("DIV"); newFillerBar.style.position = "relative"; newFillerBar.style.fontSize = "1px"; newFillerBar.style.overflow = "hidden"; newFillerBar.style.backgroundColor = this.boxColour; newFillerBar.style.backgroundImage = this.backgroundImage; switch(z)
162
+ { case "t":
163
+ if(this.topContainer)
164
+ { if(this.settings.tl.radius && this.settings.tr.radius)
165
+ { newFillerBar.style.height = topMaxRadius - this.borderWidth + "px"; newFillerBar.style.marginLeft = this.settings.tl.radius - this.borderWidth + "px"; newFillerBar.style.marginRight = this.settings.tr.radius - this.borderWidth + "px"; newFillerBar.style.borderTop = this.borderString; if(this.backgroundImage != "")
166
+ newFillerBar.style.backgroundPosition = "-" + (topMaxRadius + this.borderWidth) + "px 0px"; this.topContainer.appendChild(newFillerBar);}
167
+ this.box.style.backgroundPosition = "0px -" + (topMaxRadius - this.borderWidth) + "px";}
168
+ break; case "b":
169
+ if(this.bottomContainer)
170
+ { if(this.settings.bl.radius && this.settings.br.radius)
171
+ { newFillerBar.style.height = botMaxRadius - this.borderWidth + "px"; newFillerBar.style.marginLeft = this.settings.bl.radius - this.borderWidth + "px"; newFillerBar.style.marginRight = this.settings.br.radius - this.borderWidth + "px"; newFillerBar.style.borderBottom = this.borderString; if(this.backgroundImage != "")
172
+ newFillerBar.style.backgroundPosition = "-" + (botMaxRadius + this.borderWidth) + "px -" + (this.boxHeight + (topMaxRadius + this.borderWidth)) + "px"; this.bottomContainer.appendChild(newFillerBar);}
173
+ }
174
+ break;}
175
+ }
176
+ }
177
+ if(this.settings.autoPad == true && this.boxPadding > 0)
178
+ { var contentContainer = document.createElement("DIV"); contentContainer.style.position = "relative"; contentContainer.innerHTML = this.boxContent; contentContainer.className = "autoPadDiv"; var topPadding = Math.abs(topMaxRadius - this.boxPadding); var botPadding = Math.abs(botMaxRadius - this.boxPadding); if(topMaxRadius < this.boxPadding)
179
+ contentContainer.style.paddingTop = topPadding + "px"; if(botMaxRadius < this.boxPadding)
180
+ contentContainer.style.paddingBottom = botMaxRadius + "px"; contentContainer.style.paddingLeft = this.boxPadding + "px"; contentContainer.style.paddingRight = this.boxPadding + "px"; this.contentDIV = this.box.appendChild(contentContainer);}
181
+ }
182
+ this.drawPixel = function(intx, inty, colour, transAmount, height, newCorner, image, cornerRadius)
183
+ { var pixel = document.createElement("DIV"); pixel.style.height = height + "px"; pixel.style.width = "1px"; pixel.style.position = "absolute"; pixel.style.fontSize = "1px"; pixel.style.overflow = "hidden"; var topMaxRadius = Math.max(this.settings["tr"].radius, this.settings["tl"].radius); if(image == -1 && this.backgroundImage != "")
184
+ { pixel.style.backgroundImage = this.backgroundImage; pixel.style.backgroundPosition = "-" + (this.boxWidth - (cornerRadius - intx) + this.borderWidth) + "px -" + ((this.boxHeight + topMaxRadius + inty) -this.borderWidth) + "px";}
185
+ else
186
+ { pixel.style.backgroundColor = colour;}
187
+ if (transAmount != 100)
188
+ setOpacity(pixel, transAmount); pixel.style.top = inty + "px"; pixel.style.left = intx + "px"; newCorner.appendChild(pixel);}
189
+ }
190
+ function insertAfter(parent, node, referenceNode)
191
+ { parent.insertBefore(node, referenceNode.nextSibling);}
192
+ function BlendColour(Col1, Col2, Col1Fraction)
193
+ { var red1 = parseInt(Col1.substr(1,2),16); var green1 = parseInt(Col1.substr(3,2),16); var blue1 = parseInt(Col1.substr(5,2),16); var red2 = parseInt(Col2.substr(1,2),16); var green2 = parseInt(Col2.substr(3,2),16); var blue2 = parseInt(Col2.substr(5,2),16); if(Col1Fraction > 1 || Col1Fraction < 0) Col1Fraction = 1; var endRed = Math.round((red1 * Col1Fraction) + (red2 * (1 - Col1Fraction))); if(endRed > 255) endRed = 255; if(endRed < 0) endRed = 0; var endGreen = Math.round((green1 * Col1Fraction) + (green2 * (1 - Col1Fraction))); if(endGreen > 255) endGreen = 255; if(endGreen < 0) endGreen = 0; var endBlue = Math.round((blue1 * Col1Fraction) + (blue2 * (1 - Col1Fraction))); if(endBlue > 255) endBlue = 255; if(endBlue < 0) endBlue = 0; return "#" + IntToHex(endRed)+ IntToHex(endGreen)+ IntToHex(endBlue);}
194
+ function IntToHex(strNum)
195
+ { base = strNum / 16; rem = strNum % 16; base = base - (rem / 16); baseS = MakeHex(base); remS = MakeHex(rem); return baseS + '' + remS;}
196
+ function MakeHex(x)
197
+ { if((x >= 0) && (x <= 9))
198
+ { return x;}
199
+ else
200
+ { switch(x)
201
+ { case 10: return "A"; case 11: return "B"; case 12: return "C"; case 13: return "D"; case 14: return "E"; case 15: return "F";}
202
+ }
203
+ }
204
+ function pixelFraction(x, y, r)
205
+ { var pixelfraction = 0; var xvalues = new Array(1); var yvalues = new Array(1); var point = 0; var whatsides = ""; var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(x,2))); if ((intersect >= y) && (intersect < (y+1)))
206
+ { whatsides = "Left"; xvalues[point] = 0; yvalues[point] = intersect - y; point = point + 1;}
207
+ var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(y+1,2))); if ((intersect >= x) && (intersect < (x+1)))
208
+ { whatsides = whatsides + "Top"; xvalues[point] = intersect - x; yvalues[point] = 1; point = point + 1;}
209
+ var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(x+1,2))); if ((intersect >= y) && (intersect < (y+1)))
210
+ { whatsides = whatsides + "Right"; xvalues[point] = 1; yvalues[point] = intersect - y; point = point + 1;}
211
+ var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(y,2))); if ((intersect >= x) && (intersect < (x+1)))
212
+ { whatsides = whatsides + "Bottom"; xvalues[point] = intersect - x; yvalues[point] = 0;}
213
+ switch (whatsides)
214
+ { case "LeftRight":
215
+ pixelfraction = Math.min(yvalues[0],yvalues[1]) + ((Math.max(yvalues[0],yvalues[1]) - Math.min(yvalues[0],yvalues[1]))/2); break; case "TopRight":
216
+ pixelfraction = 1-(((1-xvalues[0])*(1-yvalues[1]))/2); break; case "TopBottom":
217
+ pixelfraction = Math.min(xvalues[0],xvalues[1]) + ((Math.max(xvalues[0],xvalues[1]) - Math.min(xvalues[0],xvalues[1]))/2); break; case "LeftBottom":
218
+ pixelfraction = (yvalues[0]*xvalues[1])/2; break; default:
219
+ pixelfraction = 1;}
220
+ return pixelfraction;}
221
+ function rgb2Hex(rgbColour)
222
+ { try{ var rgbArray = rgb2Array(rgbColour); var red = parseInt(rgbArray[0]); var green = parseInt(rgbArray[1]); var blue = parseInt(rgbArray[2]); var hexColour = "#" + IntToHex(red) + IntToHex(green) + IntToHex(blue);}
223
+ catch(e){ alert("There was an error converting the RGB value to Hexadecimal in function rgb2Hex");}
224
+ return hexColour;}
225
+ function rgb2Array(rgbColour)
226
+ { var rgbValues = rgbColour.substring(4, rgbColour.indexOf(")")); var rgbArray = rgbValues.split(", "); return rgbArray;}
227
+ function setOpacity(obj, opacity)
228
+ { opacity = (opacity == 100)?99.999:opacity; if(isSafari && obj.tagName != "IFRAME")
229
+ { var rgbArray = rgb2Array(obj.style.backgroundColor); var red = parseInt(rgbArray[0]); var green = parseInt(rgbArray[1]); var blue = parseInt(rgbArray[2]); obj.style.backgroundColor = "rgba(" + red + ", " + green + ", " + blue + ", " + opacity/100 + ")";}
230
+ else if(typeof(obj.style.opacity) != "undefined")
231
+ { obj.style.opacity = opacity/100;}
232
+ else if(typeof(obj.style.MozOpacity) != "undefined")
233
+ { obj.style.MozOpacity = opacity/100;}
234
+ else if(typeof(obj.style.filter) != "undefined")
235
+ { obj.style.filter = "alpha(opacity:" + opacity + ")";}
236
+ else if(typeof(obj.style.KHTMLOpacity) != "undefined")
237
+ { obj.style.KHTMLOpacity = opacity/100;}
238
+ }
239
+ function inArray(array, value)
240
+ { for(var i = 0; i < array.length; i++){ if (array[i] === value) return i;}
241
+ return false;}
242
+ function inArrayKey(array, value)
243
+ { for(key in array){ if(key === value) return true;}
244
+ return false;}
245
+ function addEvent(elm, evType, fn, useCapture) { if (elm.addEventListener) { elm.addEventListener(evType, fn, useCapture); return true;}
246
+ else if (elm.attachEvent) { var r = elm.attachEvent('on' + evType, fn); return r;}
247
+ else { elm['on' + evType] = fn;}
248
+ }
249
+ function removeEvent(obj, evType, fn, useCapture){ if (obj.removeEventListener){ obj.removeEventListener(evType, fn, useCapture); return true;} else if (obj.detachEvent){ var r = obj.detachEvent("on"+evType, fn); return r;} else { alert("Handler could not be removed");}
250
+ }
251
+ function format_colour(colour)
252
+ { var returnColour = "#ffffff"; if(colour != "" && colour != "transparent")
253
+ { if(colour.substr(0, 3) == "rgb")
254
+ { returnColour = rgb2Hex(colour);}
255
+ else if(colour.length == 4)
256
+ { returnColour = "#" + colour.substring(1, 2) + colour.substring(1, 2) + colour.substring(2, 3) + colour.substring(2, 3) + colour.substring(3, 4) + colour.substring(3, 4);}
257
+ else
258
+ { returnColour = colour;}
259
+ }
260
+ return returnColour;}
261
+ function get_style(obj, property, propertyNS)
262
+ { try
263
+ { if(obj.currentStyle)
264
+ { var returnVal = eval("obj.currentStyle." + property);}
265
+ else
266
+ { if(isSafari && obj.style.display == "none")
267
+ { obj.style.display = ""; var wasHidden = true;}
268
+ var returnVal = document.defaultView.getComputedStyle(obj, '').getPropertyValue(propertyNS); if(isSafari && wasHidden)
269
+ { obj.style.display = "none";}
270
+ }
271
+ }
272
+ catch(e)
273
+ { }
274
+ return returnVal;}
275
+ function getElementsByClass(searchClass, node, tag)
276
+ { var classElements = new Array(); if(node == null)
277
+ node = document; if(tag == null)
278
+ tag = '*'; var els = node.getElementsByTagName(tag); var elsLen = els.length; var pattern = new RegExp("(^|\s)"+searchClass+"(\s|$)"); for (i = 0, j = 0; i < elsLen; i++)
279
+ { if(pattern.test(els[i].className))
280
+ { classElements[j] = els[i]; j++;}
281
+ }
282
+ return classElements;}
283
+ function newCurvyError(errorMessage)
284
+ { return new Error("curvyCorners Error:\n" + errorMessage)
285
+ }